{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7289ZOYE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7289ZOYE",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12"
],
"assay_term": {
"@id": "/assay-terms/NTR_0000745/",
"status": "released",
"term_name": "single nucleus methylation and chromatin conformation capture sequencing"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7289ZOYE](/measurement-sets/IGVFDS7289ZOYE/) has sequence file(s): [IGVFFI4489UPSY](/sequence-files/IGVFFI4489UPSY/), [IGVFFI5639ZYDB](/sequence-files/IGVFFI5639ZYDB/), [IGVFFI2790JUIP](/sequence-files/IGVFFI2790JUIP/), [IGVFFI6504RTQF](/sequence-files/IGVFFI6504RTQF/), [IGVFFI7748KFHE](/sequence-files/IGVFFI7748KFHE/), [IGVFFI7277DXGO](/sequence-files/IGVFFI7277DXGO/), [IGVFFI8703ZLUH](/sequence-files/IGVFFI8703ZLUH/), [IGVFFI9698OXVX](/sequence-files/IGVFFI9698OXVX/), [IGVFFI3845WOAH](/sequence-files/IGVFFI3845WOAH/), [IGVFFI3540GJSH](/sequence-files/IGVFFI3540GJSH/), [IGVFFI6835QCMX](/sequence-files/IGVFFI6835QCMX/), [IGVFFI9186MCOG](/sequence-files/IGVFFI9186MCOG/), [IGVFFI7095FJRU](/sequence-files/IGVFFI7095FJRU/), [IGVFFI1000DHIL](/sequence-files/IGVFFI1000DHIL/), [IGVFFI2244UGMY](/sequence-files/IGVFFI2244UGMY/), [IGVFFI1381WIZJ](/sequence-files/IGVFFI1381WIZJ/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS7289ZOYE/"
},
{
"category": "NTR term ID",
"detail": "Assay term for [NTR_0000745](/assay-terms/NTR_0000745/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/assay-terms/NTR_0000745/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS7289ZOYE](/measurement-sets/IGVFDS7289ZOYE/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS7289ZOYE/"
}
]
},
"award": {
"@id": "/awards/HG012079/",
"component": "networks",
"contact_pi": {
"@id": "/users/53ea51d1-5c61-4f1e-99fb-ef857bd652a3/",
"title": "Chongyuan Luo"
},
"title": "Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotency"
},
"control_for": [],
"creation_timestamp": "2024-11-15T19:29:19.297237+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3754NCBP/",
"accession": "IGVFDO3754NCBP",
"aliases": [
"chongyuan-luo:C29"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4489UPSY/",
"accession": "IGVFFI4489UPSY",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T04:11:43.608311+00:00",
"file_format": "fastq",
"file_size": 2802358227,
"href": "/sequence-files/IGVFFI4489UPSY/@@download/IGVFFI4489UPSY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/41f8302f-c683-48d1-8773-8b068a88e8b7/IGVFFI4489UPSY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5639ZYDB/",
"accession": "IGVFFI5639ZYDB",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T03:48:34.372014+00:00",
"file_format": "fastq",
"file_size": 2693396242,
"href": "/sequence-files/IGVFFI5639ZYDB/@@download/IGVFFI5639ZYDB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/f6b9311a-b842-45f5-8710-677c4c421534/IGVFFI5639ZYDB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2790JUIP/",
"accession": "IGVFFI2790JUIP",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T05:00:05.125117+00:00",
"file_format": "fastq",
"file_size": 2806579034,
"href": "/sequence-files/IGVFFI2790JUIP/@@download/IGVFFI2790JUIP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/876497b1-6228-4f33-857f-b1cff5c21328/IGVFFI2790JUIP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6504RTQF/",
"accession": "IGVFFI6504RTQF",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T04:22:16.944259+00:00",
"file_format": "fastq",
"file_size": 2868518459,
"href": "/sequence-files/IGVFFI6504RTQF/@@download/IGVFFI6504RTQF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/2455e18f-a618-4f22-854b-8610d7a64bbf/IGVFFI6504RTQF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7748KFHE/",
"accession": "IGVFFI7748KFHE",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T03:58:41.805194+00:00",
"file_format": "fastq",
"file_size": 2733085755,
"href": "/sequence-files/IGVFFI7748KFHE/@@download/IGVFFI7748KFHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/eebb6f35-11e5-4155-8887-cf65b47884b5/IGVFFI7748KFHE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7277DXGO/",
"accession": "IGVFFI7277DXGO",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T04:36:04.336599+00:00",
"file_format": "fastq",
"file_size": 2796018311,
"href": "/sequence-files/IGVFFI7277DXGO/@@download/IGVFFI7277DXGO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/6ef0b4c8-5beb-448a-ba97-5a3a3d2ea97f/IGVFFI7277DXGO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8703ZLUH/",
"accession": "IGVFFI8703ZLUH",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T04:46:31.066865+00:00",
"file_format": "fastq",
"file_size": 2863439181,
"href": "/sequence-files/IGVFFI8703ZLUH/@@download/IGVFFI8703ZLUH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/0ce0fba7-5564-4f72-8015-0e14563086ef/IGVFFI8703ZLUH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9698OXVX/",
"accession": "IGVFFI9698OXVX",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T05:11:41.498235+00:00",
"file_format": "fastq",
"file_size": 2857525548,
"href": "/sequence-files/IGVFFI9698OXVX/@@download/IGVFFI9698OXVX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/0c0e3fb6-603a-4e2a-b6bc-ac2030f96387/IGVFFI9698OXVX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3845WOAH/",
"accession": "IGVFFI3845WOAH",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T05:25:43.688500+00:00",
"file_format": "fastq",
"file_size": 2855961617,
"href": "/sequence-files/IGVFFI3845WOAH/@@download/IGVFFI3845WOAH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/1d2e7ca0-30d9-40b2-bc12-d6c641c25688/IGVFFI3845WOAH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3540GJSH/",
"accession": "IGVFFI3540GJSH",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T05:36:37.071843+00:00",
"file_format": "fastq",
"file_size": 2926447634,
"href": "/sequence-files/IGVFFI3540GJSH/@@download/IGVFFI3540GJSH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/500f3167-76b6-4334-bcde-fbb635134126/IGVFFI3540GJSH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6835QCMX/",
"accession": "IGVFFI6835QCMX",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T05:50:15.476652+00:00",
"file_format": "fastq",
"file_size": 2858232426,
"href": "/sequence-files/IGVFFI6835QCMX/@@download/IGVFFI6835QCMX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/cc19c054-5be6-4e11-894f-44534041bccf/IGVFFI6835QCMX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9186MCOG/",
"accession": "IGVFFI9186MCOG",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T06:02:35.559708+00:00",
"file_format": "fastq",
"file_size": 2919426172,
"href": "/sequence-files/IGVFFI9186MCOG/@@download/IGVFFI9186MCOG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/1b42cc7f-651f-4d1b-b08d-2893cb6af340/IGVFFI9186MCOG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7095FJRU/",
"accession": "IGVFFI7095FJRU",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T06:16:04.488539+00:00",
"file_format": "fastq",
"file_size": 2834928401,
"href": "/sequence-files/IGVFFI7095FJRU/@@download/IGVFFI7095FJRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/e0158a13-d14c-455d-bab1-61b896d1fdd9/IGVFFI7095FJRU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1000DHIL/",
"accession": "IGVFFI1000DHIL",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T06:28:22.835117+00:00",
"file_format": "fastq",
"file_size": 2903668766,
"href": "/sequence-files/IGVFFI1000DHIL/@@download/IGVFFI1000DHIL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/8bfe994f-c79e-44ef-8e79-f550cb08de5f/IGVFFI1000DHIL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2244UGMY/",
"accession": "IGVFFI2244UGMY",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T06:41:12.665972+00:00",
"file_format": "fastq",
"file_size": 2733855778,
"href": "/sequence-files/IGVFFI2244UGMY/@@download/IGVFFI2244UGMY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/b525a1de-52aa-4da1-9ee9-310b5b7a751d/IGVFFI2244UGMY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1381WIZJ/",
"accession": "IGVFFI1381WIZJ",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day12_L8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T06:52:51.615703+00:00",
"file_format": "fastq",
"file_size": 2776170743,
"href": "/sequence-files/IGVFFI1381WIZJ/@@download/IGVFFI1381WIZJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/d12e3bd7-673b-4d15-99d1-5da0ba6aa704/IGVFFI1381WIZJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snm3c/yzcl47/20231005-3C29D12-Pos1-B06_S16_L008_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/chongyuan-luo/",
"title": "Chongyuan Luo, UCLA"
},
"preferred_assay_title": "snM3C-seq",
"protocols": [
"https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1"
],
"release_timestamp": "2025-02-11T00:54:50.266070+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9153SKDZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9153SKDZ",
"aliases": [
"chongyuan-luo:C29_day12"
],
"classifications": [
"reprogrammed cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000057/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "fibroblast",
"term_name": "fibroblast"
}
],
"status": "released",
"summary": "fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 12 days, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/EFO_0004905/",
"status": "released",
"term_name": "induced pluripotent stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "24",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2024-11-16T03:48:34.372014+00:00",
"summary": "snM3C-seq",
"uuid": "e20f6082-fa87-4b97-967c-b03b3c16b044"
}